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Arjun Prasad edited this page Sep 12, 2019 · 28 revisions

NCBI Antimicrobial Resistance Gene Finder Plus (AMRFinderPlus)

See Version 1 documentation for the most recent non-development release. We will continue to support version 1 until AMRFinderPlus has been more thoroughly tested and is ready for full release.

Overview for AMRFinderPlus 3.1

This software and the accompanying database are designed to find acquired antimicrobial resistance genes in bacterial protein or assembled nucleotide sequences as well as known point mutations for several taxa. With AMRFinderPlus we have added select members of additional classes of genes such as virulence factors, biocide, heat, acid, and metal resistance genes.

NOTE This is beta software still under active development. Once AMRFinderPlus is available as a full release we will no longer support the original version of AMRFinder. By default the results returned by AMRFinderPlus will be similar to those returned by AMRFinder with some additional data on function. See Running AMRFinderPlus for information on how to get the additional hit types.

New in version 3.1-beta (AMRFinderPlus)

  • New blacklisted gene feature to remove hits for common "--plus" genes generally uninformative for a given taxon
  • New database file to enable the blacklisting

Installation

AMRFinder requires BLAST and HMMER. We provide instructions using BioConda to install the prerequisites.

Installation Instructions

Methods

AMRFinder can be run in multiple modes with protein sequence as input and/or with DNA sequence as input. To get maximum information it should be run with both protein and nucleotide. When run with protein sequence it uses both BLASTP and HMMER to search protein sequences for AMR genes along with a hierarchical tree of gene families to classify and name novel sequences. With nucleotide sequences it uses BLASTX translated searches and the hierarchical tree of gene families. Adding the --organism option enables screening for point mutations in select organisms.

Running AMRFinderPlus
Methods
AMRFinderPlus database
Interpreting results

Related Resources

The Pathogen Detection team at NCBI has curated other AMR Resources we encourage you to check out. Most notably the data used by AMRFinder in a table form with additional metadata is available in the Reference Gene Catalog and as a tab-delimited file Reference Gene Catalog on FTP.

Help

Subscribe to the amrfinder-announce mailing list to get updates when we release new versions of the software or database. This is a low-traffic list.

Note that this version of AMRFinderPlus is an alpha version. If you have any questions about or experience problems running AMRFinderPlus, please contact pd-help@ncbi.nlm.nih.gov.

Licenses

Publication

See our our AMRFinder paper for more details.

Citation

Feldgarden, M., Brover, V., Haft, D.H., Prasad, A.B., Slotta, D.J., Tolstoy, I., Tyson, G.H., Zhao, S., Hsu, C.-H., McDermott, P.F., Tadesse, D.A., Morales, C., Simmons, M., Tillman, G., Wasilenko, J., Folster, J.P., Klimke, W., 2019. Validating the NCBI AMRFinder Tool and Resistance Gene Database Using Antimicrobial Resistance Genotype-Phenotype Correlations in a Collection of NARMS Isolates. Antimicrob. Agents Chemother. https://doi.org/10.1128/AAC.00483-19.

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